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Molecular Phylogeny of Poaceae
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Molecular Phylogeny of Poaceae

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Molecular Biology".

Deadline for manuscript submissions: closed (31 December 2024) | Viewed by 3323

Special Issue Editors

Prof. Dr. Alexander V. Rodionov

E-Mail Website
Guest Editor
Komarov Botanical Institute of the Russian Academy of Sciences, 197022 St. Petersburg, Russia
Interests: Poaceae; genome evolution; plant molecular phylogeny
Dr. Victoria Shneyer

E-Mail Website
Guest Editor
Komarov Botanical Institute of the Russian Academy of Sciences, 197022 St. Petersburg, Russia
Interests: plant systematics; molecular phylogeny; polyploidy; cryptic species; speciation; DNA barcoding
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Grasses are the main food and fodder crops. In order to increase crop yield and resistance to various factors, modern breeding technology is actively searching for necessary genes among the relatives of cultivated plants, both close and distant. Therefore, it is necessary to gain a comprehensive understanding of the relationship between species, genera, and families of grasses. Molecular methods have already helped to refine and, in some cases, to revise earlier taxonomic ideas. The utilization of modern effective methods makes it possible to accelerate the process of improving our knowledge of the Poaceae phylogeny.

Prof. Dr. Alexander V. Rodionov
Dr. Victoria Shneyer
Guest Editors

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Keywords

  • Poaceae
  • grass family
  • evolutionary relationships
  • molecular phylogeny
  • phylogenetic analysis
  • chloroplast DNA markers
  • nuclear markers
  • comparative genomics

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Published Papers (2 papers)

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Research

23 pages, 7454 KiB  
Article
Comprehensive Identification and Expression Analysis of the Multidrug and Toxic Compound Extrusion (MATE) Gene Family in Brachypodium distachyon
by Sirui Ma, Yixian Guo, Tianyi Zhang, Di Liu, Linna Wang, Ruiwen Hu, Demian Zhou, Ying Zhou, Qinfang Chen and Lujun Yu
Plants 2024, 13(18), 2586; https://doi.org/10.3390/plants13182586 - 15 Sep 2024
Cited by 23 | Viewed by 1477
Abstract
The Multidrug and Toxic Compound Extrusion (MATE) proteins serve as pivotal transporters responsible for the extrusion of metabolites, thereby playing a significant role in both plant development and the detoxification of toxins. The MATE gene family within the Brachypodium distachyon, which is [...] Read more.
The Multidrug and Toxic Compound Extrusion (MATE) proteins serve as pivotal transporters responsible for the extrusion of metabolites, thereby playing a significant role in both plant development and the detoxification of toxins. The MATE gene family within the Brachypodium distachyon, which is an important model organism of the Poaceae family, remains largely unexplored. Here, a comprehensive identification and analysis of MATE genes that complement B. distachyon were conducted. The BdMATE genes were systematically categorized into five distinct groups, predicated on an assessment of their phylogenetic affinities and protein structure. Furthermore, our investigation revealed that dispersed duplication has significantly contributed to the expansion of the BdMATE genes, with tandem and segmental duplications showing important roles, suggesting that the MATE genes in Poaceae species have embarked on divergent evolutionary trajectories. Examination of ω values demonstrated that BdMATE genes underwent purifying selection throughout the evolutionary process. Furthermore, collinearity analysis has confirmed a high conservation of MATE genes between B. distachyon and rice. The cis-regulatory elements analysis within BdMATEs promoters, coupled with expression patterns, suggests that BdMATEs play important roles during plant development and in response to phytohormones. Collectively, the findings presented establish a foundational basis for the subsequent detailed characterization of the MATE gene family members in B. distachyon. Full article
(This article belongs to the Special Issue Molecular Phylogeny of Poaceae)
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21 pages, 5787 KiB  
Article
Hybridization in the Subtribe Alopecurinae Dumort. (Poaceae) According to Molecular Phylogenetic Analysis: Different Ploidy Level Tells Different Origin of the Groups
by Alexander A. Gnutikov, Nikolai N. Nosov, Elizaveta O. Punina, Igor G. Loskutov, Victoria S. Shneyer, Sergei A. Chekrygin and Alexander V. Rodionov
Plants 2024, 13(7), 919; https://doi.org/10.3390/plants13070919 - 22 Mar 2024
Cited by 2 | Viewed by 1253
Abstract
We performed next-generation sequencing of the 18S rDNA–ITS1–5.8S rDNA region along with traditional Sanger sequencing of rbcL, matK, ndhF, and ITS1–5.8S rDNA–ITS2 to clarify the hybridization pattern in the subtribe Alopecurinae and in the genus Alopecurus in particular. Our data [...] Read more.
We performed next-generation sequencing of the 18S rDNA–ITS1–5.8S rDNA region along with traditional Sanger sequencing of rbcL, matK, ndhF, and ITS1–5.8S rDNA–ITS2 to clarify the hybridization pattern in the subtribe Alopecurinae and in the genus Alopecurus in particular. Our data support the hybrid origin of Alopecurus × brachystylus from hybridization between A. geniculatus (sect. Alopecurium) and A. pratensis (sect. Alopecurus). Moreover, in the rDNA of hybrid A. × brachystylus, only A. aequalis-like ribotypes from tetraploid A. geniculatus participated. Surprisingly, we found the traces of introgression of A. arundinaceus-like ribotypes not only in hybrid A. × marssonii (A. geniculatus × A. arundinaceus) but in A. aequalis s. str. as well. A high-polyploid group from the section Alopecurus, A. aggr. alpinus has undoubted hybrid origin: e. g., A. brachystachyus has rDNA from the sect. Alopecurium. Alopecurus alpinus, with its allies, is clearly distinct from other members of the sect. Alopecurus (especially by maternal line) and thus we can re-establish a previous opinion about the separate group to which A. alpinus belongs. Species from the section Colobachne (presumably Alpine grasses from Ancient Mediterranean region) probably hybridized with the A. alpinus group. Even A. myosuroides (sect. Pseudophalaris) that could be referred to the separate genus has ribotypes common with the species of the section Alopecurium (A. aequalis, A. geniculatus) in one of the accessions. Additionally, we found that the possible polyphyletic origin of the genus Limnas. Limnas stelleri is very close to Alopecurus magellanicus according to NGS data, while L. malyschevii is more or less distinct from other studied species of the genus Alopecurus. Full article
(This article belongs to the Special Issue Molecular Phylogeny of Poaceae)
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